libbpp-phyl →
2.3.1-10 →
armhf → 2017-08-31 16:46:08
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| libbpp-phyl 2.3.1-10 (armhf) Thu, 31 Aug 2017 14:54:49 +0000 |
+==============================================================================+
Package: libbpp-phyl
Version: 2.3.1-10
Source Version: 2.3.1-10
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-8ea3540e-1909-4988-a6d6-5e19e33ab4f3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.0 MB]
Fetched 22.1 MB in 25s (856 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'libbpp-phyl' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/libbpp-phyl.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/libbpp-phyl.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 597 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main libbpp-phyl 2.3.1-10 (dsc) [2174 B]
Get:2 http://172.17.0.1/private buster-staging/main libbpp-phyl 2.3.1-10 (tar) [587 kB]
Get:3 http://172.17.0.1/private buster-staging/main libbpp-phyl 2.3.1-10 (diff) [8312 B]
Fetched 597 kB in 0s (7325 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libbpp-phyl-tW2HMw/libbpp-phyl-2.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libbpp-phyl-tW2HMw' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-BFpKoe/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-BFpKoe/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-BFpKoe/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (2991 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 32 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14868 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), cmake, d-shlibs (>= 0.80), libbpp-seq-dev (>= 2.3.1)
Filtered Build-Depends: debhelper (>= 10), cmake, d-shlibs (>= 0.80), libbpp-seq-dev (>= 2.3.1)
dpkg-deb: building package 'sbuild-build-depends-libbpp-phyl-dummy' in '/<<BUILDDIR>>/resolver-BFpKoe/apt_archive/sbuild-build-depends-libbpp-phyl-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libbpp-phyl-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Sources [520 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ Packages [600 B]
Fetched 2453 B in 0s (3558 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install libbpp-phyl build dependencies (apt-based resolver)
-----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libbpp-core-dev libbpp-core3 libbpp-seq-dev libbpp-seq11 libbsd0 libcroco3
libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libldap-2.4-2 libldap-common liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtimedate-perl
libtool libuv1 libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff lrzip krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libbpp-core-dev libbpp-core3 libbpp-seq-dev libbpp-seq11 libbsd0 libcroco3
libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libldap-2.4-2 libldap-common liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtimedate-perl
libtool libuv1 libxml2 m4 man-db po-debconf
sbuild-build-depends-libbpp-phyl-dummy
0 upgraded, 58 newly installed, 0 to remove and 32 not upgraded.
Need to get 28.0 MB of archives.
After this operation, 110 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-BFpKoe/apt_archive ./ sbuild-build-depends-libbpp-phyl-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.9.0-1 [1294 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3.1 [609 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-2 [254 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.45+dfsg-1 [87.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1 [197 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.25.0-1 [70.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.18.0-2 [42.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2l-2 [893 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.55.0-1 [264 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.4-3 [94.7 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.9.1-3 [73.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.9.0-1 [2509 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.31-1 [223 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.31-1 [105 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.31-1 [63.5 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2.1 [736 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf d-shlibs all 0.81 [18.7 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.53.4-3 [2628 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.7.2 [975 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libbpp-core3 armhf 2.3.1-5 [499 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libbpp-core-dev armhf 2.3.1-5 [918 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libbpp-seq11 armhf 2.3.1-8 [405 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libbpp-seq-dev armhf 2.3.1-8 [705 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29-4+rpi1 dpkg-dev_1.18.24 g++-7_7.1.0-13+rpi1 gcc-7_7.1.0-13+rpi1 libc6-dev_2.24-12 libstdc++-7-dev_7.1.0-13+rpi1 libstdc++6_7.1.0-13+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.116 apt_1.5~beta1+b3 autoconf_2.69-11 automake_1:1.15.1-2.1 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.29-4+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 cmake_3.9.0-1 cmake-data_3.9.0-1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.1.0-2 cpp-7_7.1.0-13+rpi1 d-shlibs_0.81 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.7.2 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-3.1 file_1:5.31-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-2 g++-7_7.1.0-13+rpi1 gcc_4:7.1.0-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.1.0-13+rpi1 gcc-7-base_7.1.0-13+rpi1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-10 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libarchive13_3.2.2-2 libasan4_7.1.0-13+rpi1 libassuan0_2.4.3-3 libatomic1_7.1.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-2+rpi1 libbpp-core-dev_2.3.1-5 libbpp-core3_2.3.1-5 libbpp-seq-dev_2.3.1-8 libbpp-seq11_2.3.1-8 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-13+rpi1 libcilkrts5_7.1.0-13+rpi1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3_7.55.0-1 libdb5.3_5.3.28-13+rpi1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libexpat1_2.2.3-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.1.0-13+rpi1 libgcc1_1:7.1.0-13+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-13+rpi1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.25.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-5 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.31-1 libprocps6_2:3.3.12-3 libpsl5_0.18.0-2 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librhash0_1.3.4-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.5-1 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-4 libstdc++-7-dev_7.1.0-13+rpi1 libstdc++6_7.1.0-13+rpi1 libsystemd0_234-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-13+rpi1 libudev1_234-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libuv1_1.9.1-3 libxml2_2.9.4+dfsg1-3.1 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-4 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-5 perl-base_5.26.0-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-5 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbpp-phyl-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-2 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_234-2 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Aug 25 11:53:12 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libbpp-phyl_2.3.1-10.dsc
dpkg-source: info: extracting libbpp-phyl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libbpp-phyl_2.3.1.orig.tar.gz
dpkg-source: info: unpacking libbpp-phyl_2.3.1-10.debian.tar.xz
dpkg-source: info: applying unforce-cxxflags.patch
dpkg-source: info: applying relax_test_timeout.patch
dpkg-source: info: applying 0002-Fixed-unit-tests-compilation-on-some-platforms.patch
dpkg-source: info: applying remove_deprecated_warnings.patch
dpkg-source: info: applying test_likelihood_clock.patch
dpkg-source: info: applying test_mapping.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-8ea3540e-1909-4988-a6d6-5e19e33ab4f3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libbpp-phyl
dpkg-buildpackage: info: source version 2.3.1-10
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build libbpp-phyl-2.3.1
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-- The CXX compiler identification is GNU 7.1.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- bpp-core 3.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
-- includes: /usr/include
-- bpp-seq 11.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0
-- includes: /usr/include
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend
make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target bpp-phyl-shared
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build
Scanning dependencies of target bpp-phyl-static
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:243:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
map<string, bool> BipartitionList::getBipartition(size_t i) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:262:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* BipartitionList::getBitBipartition(size_t i) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:294:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::addBipartition(map<string, bool>& bipart, bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:320:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::deleteBipartition(size_t i) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:331:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::containsBipartition(map<string, bool>& bipart, bool checkElements) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:369:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areIdentical(size_t k1, size_t k2) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:403:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areCompatible(size_t k1, size_t k2) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:454:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areAllCompatibleWith(map<string, bool>& bipart, bool checkElements) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:528:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t BipartitionList::getPartitionSize(size_t k) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:605:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::flip(size_t k) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:650:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* BipartitionList::toTree() const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:129:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:207:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:267:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<BipartitionList*>& vecBipartL) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:331:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<BipartitionList*>& vecBipartL) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOMultiTreeReaderFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeWriterFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOMultiTreeWriterFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:57:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:59:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeReaderFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOMultiTreeReaderFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOTreeWriterFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOMultiTreeWriterFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:57:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:59:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/../Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:104:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:128:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:165:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:194:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:223:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:313:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:349:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:104:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:699:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:734:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:128:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:165:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:194:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:223:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:313:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:349:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1157:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:699:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:734:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1399:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1425:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1157:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1399:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1425:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn) throw (Exception)
^~~~~
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:243:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
map<string, bool> BipartitionList::getBipartition(size_t i) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:262:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* BipartitionList::getBitBipartition(size_t i) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:294:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::addBipartition(map<string, bool>& bipart, bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:320:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::deleteBipartition(size_t i) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:331:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::containsBipartition(map<string, bool>& bipart, bool checkElements) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:369:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areIdentical(size_t k1, size_t k2) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:403:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areCompatible(size_t k1, size_t k2) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:454:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool BipartitionList::areAllCompatibleWith(map<string, bool>& bipart, bool checkElements) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:528:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t BipartitionList::getPartitionSize(size_t k) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:605:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BipartitionList::flip(size_t k) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.cpp:650:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* BipartitionList::toTree() const throw (Exception)
^~~~~
[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:129:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:207:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkElements) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:267:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<BipartitionList*>& vecBipartL) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.cpp:331:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<BipartitionList*>& vecBipartL) throw (Exception)
^~~~~
[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:53:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAgglomerativeDistanceMethod::setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:62:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAgglomerativeDistanceMethod::computeTree() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:53:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAgglomerativeDistanceMethod::setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:62:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractAgglomerativeDistanceMethod::computeTree() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:83:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:101:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:106:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:60:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BioNJ::computeTree() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:83:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:101:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:106:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.cpp:60:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void BioNJ::computeTree() throw (Exception)
^~~~~
[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:73:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:188:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:297:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::applyParameters() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:323:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:412:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:419:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::initTreeLikelihoods(const SequenceContainer& sequences) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:591:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:622:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:652:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DistanceEstimation::computeMatrix() throw (NullPointerException)
^~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:73:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:188:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:297:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::applyParameters() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:323:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:412:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:419:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TwoTreeLikelihood::initTreeLikelihoods(const SequenceContainer& sequences) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:591:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:622:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:652:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DistanceEstimation::computeMatrix() throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:88:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
HierarchicalClustering(const std::string& method, const DistanceMatrix& matrix, bool verbose = false) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:105:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:60:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<size_t> HierarchicalClustering::getBestPair() throw (Exception)
^~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:51:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> NeighborJoining::getBestPair() throw (Exception)
^~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::ClusterInfos>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:88:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
HierarchicalClustering(const std::string& method, const DistanceMatrix& matrix, bool verbose = false) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:105:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:60:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<size_t> HierarchicalClustering::getBestPair() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:84:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PGMA(const DistanceMatrix& matrix, bool weighted = true, bool verbose = true) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:97:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:108:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:60:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<size_t> PGMA::getBestPair() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.cpp:51:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> NeighborJoining::getBestPair() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:50:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractDendrogramPlot::plot(GraphicDevice& gDevice) const throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::PGMAInfos>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::ClusterInfos>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:84:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PGMA(const DistanceMatrix& matrix, bool weighted = true, bool verbose = true) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:97:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:108:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:60:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<size_t> PGMA::getBestPair() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:71:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:107:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:72:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CladogramPlot::drawDendrogram_(GraphicDevice& gDevice) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:50:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractDendrogramPlot::plot(GraphicDevice& gDevice) const throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/PGMA.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::PGMAInfos>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:104:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:75:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PhylogramPlot::drawDendrogram_(GraphicDevice& gDevice) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addListener(const std::string& propertyName, TreeDrawingListener* listener) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:109:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void enableListener(const std::string& propertyName, bool tf) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:116:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isListenerEnabled(const std::string& propertyName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:123:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerTreeDrawing(TreeDrawing* td) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:162:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicTreeDrawingDisplayControler(const TreeDrawingSettings* settings) throw (NullPointerException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:56:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeDrawingDisplayControler::addListener(const std::string& propertyName, TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:71:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.h:107:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:72:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void CladogramPlot::drawDendrogram_(GraphicDevice& gDevice) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:67:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:67:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:53:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* BppOMultiTreeReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:102:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addListener(const std::string& propertyName, TreeDrawingListener* listener) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:109:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void enableListener(const std::string& propertyName, bool tf) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:116:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isListenerEnabled(const std::string& propertyName) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:123:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void registerTreeDrawing(TreeDrawing* td) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:162:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BasicTreeDrawingDisplayControler(const TreeDrawingSettings* settings) throw (NullPointerException) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:56:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeDrawingDisplayControler::addListener(const std::string& propertyName, TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:75:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void plot(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:78:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.h:104:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void drawDendrogram_(GraphicDevice& gDevice) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:75:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PhylogramPlot::drawDendrogram_(GraphicDevice& gDevice) const throw (Exception)
^~~~~
[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:335:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void plot(GraphicDevice& gDevice) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:344:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:353:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:366:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawing.h:367:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:228:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Point2D<double> getNodePosition(int nodeId) const throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:230:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getNodeAt(const Point2D<double>& position) const throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:273:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDisplaySettings(const TreeDrawingSettings* tds) throw (NullPointerException) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:288:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void collapseNode(int nodeId, bool yn) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:294:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:300:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void removeTreeDrawingListener(TreeDrawingListener* listener) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:53:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* BppOMultiTreeWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
/usr/include/c++/7/bits/vector.tcc: In member function 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:67:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:67:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43,
from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp:53:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IMultiTree* BppOMultiTreeReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43,
from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const string&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/MG94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/YNGP_M1.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:71:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/RE08.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h:83:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/TS98.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:72:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:87:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Nucleotide/YpR.h:131:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:105:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FromMixtureSubstitutionModel.h:174:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:106:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp:53:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OMultiTree* BppOMultiTreeWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:110:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:1704:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SiteContainer* data) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void bpp::BppOFrequenciesSetFormat::initialize_(bpp::FrequenciesSet&, const bpp::SiteContainer*)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43,
from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:53:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* BppOTreeReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43,
from /usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual bpp::DiscreteDistribution* bpp::BppORateDistributionFormat::read(const string&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:53:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* BppOTreeWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/MG94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/YNGP_M1.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:71:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/RE08.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/TS98.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:72:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:87:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Nucleotide/YpR.h:131:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:105:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FromMixtureSubstitutionModel.h:174:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:106:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:86:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:108:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:94:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:117:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:125:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:139:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:160:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:167:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:110:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:88:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IDistanceMatrix* createReader(const std::string& format, bool extended=false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:99:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ODistanceMatrix * createWriter(const std::string& format, bool extended=false) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:70:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:74:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:76:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:80:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:47:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IDistanceMatrix* IODistanceMatrixFactory::createReader(const std::string& format, bool extended) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:53:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ODistanceMatrix* IODistanceMatrixFactory::createWriter(const std::string& format, bool extended) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:1704:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SiteContainer* data) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:110:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:132:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:164:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:175:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:202:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:234:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:264:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:292:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:491:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:521:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:544:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:599:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:625:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int warn = 1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:46:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IFrequenciesSet* IOFrequenciesSetFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:52:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OFrequenciesSet* IOFrequenciesSetFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* read(const std::string& description) throw (Exception);
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp:53:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* BppOTreeReaderFormat::read(const std::string& description) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:81:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:95:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& modelName = "") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:104:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModel(const bpp::TreeLikelihood& treelikelihood) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:113:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModels(const PairedSiteLikelihoods& psl) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:141:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::size_t getNumberOfSites() const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:76:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static PairedSiteLikelihoods read(std::istream& is) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:83:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static PairedSiteLikelihoods read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:117:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<double> read(std::istream& is) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:123:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<double> read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:56:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read(std::istream& is) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:131:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read(const std::string& path) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:230:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<double> IOPhymlPairedSiteLikelihoods::read(std::istream& is) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:270:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<double> IOPhymlPairedSiteLikelihoods::read(const std::string& path) throw (Exception)
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:46:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISubstitutionModel* IOSubstitutionModelFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:52:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSubstitutionModel* IOSubstitutionModelFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h:83:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* read(const std::string& description) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In static member function 'static std::vector<double> bpp::IOPhymlPairedSiteLikelihoods::read(std::istream&)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::PairedSiteLikelihoods bpp::IOTreepuzzlePairedSiteLikelihoods::read(std::istream&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp:53:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* BppOTreeWriterFormat::read(const std::string& description) throw (Exception)
^~~~~
[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:51:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* IOTreeFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:59:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* IOTreeFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:86:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:94:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:117:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:125:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:139:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:160:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:167:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:88:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IDistanceMatrix* createReader(const std::string& format, bool extended=false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:99:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ODistanceMatrix * createWriter(const std::string& format, bool extended=false) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:70:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:74:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:76:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:80:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:47:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IDistanceMatrix* IODistanceMatrixFactory::createReader(const std::string& format, bool extended) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:53:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ODistanceMatrix* IODistanceMatrixFactory::createWriter(const std::string& format, bool extended) throw (Exception)
^~~~~
[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:69:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node> * Newick::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:96:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:113:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:129:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::read(istream& in, vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:155:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:175:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:86:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual IFrequenciesSet* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h:95:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OFrequenciesSet * createWriter(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:46:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
IFrequenciesSet* IOFrequenciesSetFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp:52:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OFrequenciesSet* IOFrequenciesSetFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp
[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:75:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node> * NexusIOTree::read(istream &in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:88:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:167:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:177:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:186:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:251:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:81:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:95:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& modelName = "") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:104:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModel(const bpp::TreeLikelihood& treelikelihood) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:113:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModels(const PairedSiteLikelihoods& psl) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:141:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::size_t getNumberOfSites() const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:76:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static PairedSiteLikelihoods read(std::istream& is) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:83:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static PairedSiteLikelihoods read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:117:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<double> read(std::istream& is) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h:123:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<double> read(const std::string& path) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:56:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read(std::istream& is) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:131:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read(const std::string& path) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:230:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<double> IOPhymlPairedSiteLikelihoods::read(std::istream& is) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:270:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<double> IOPhymlPairedSiteLikelihoods::read(const std::string& path) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:99:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* Nhx::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:126:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::read(istream& in, vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:189:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:201:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Nhx::Element Nhx::getElement(const string& elt) const throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:329:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* Nhx::parenthesisToTree(const string& description) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:348:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string Nhx::propertyToString_(const Clonable* pptObject, short type) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:381:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* Nhx::stringToProperty_(const string& pptDesc, short type) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp
/usr/include/c++/7/bits/vector.tcc: In static member function 'static std::vector<double> bpp::IOPhymlPairedSiteLikelihoods::read(std::istream&)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::PairedSiteLikelihoods bpp::IOTreepuzzlePairedSiteLikelihoods::read(std::istream&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:86:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:94:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:117:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:125:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:139:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:160:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:167:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:70:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:74:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:76:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:80:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:56:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix * PhylipDistanceMatrixFormat::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:96:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PhylipDistanceMatrixFormat::write(const DistanceMatrix& dist, ostream& out) const throw (Exception)
^~~~~
[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:87:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ISubstitutionModel* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h:96:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OSubstitutionModel * createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h:201:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize_(TransitionModel& model, const SiteContainer* data) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:46:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ISubstitutionModel* IOSubstitutionModelFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp:52:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OSubstitutionModel* IOSubstitutionModelFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:83:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ITree* createReader(const std::string& format) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.h:92:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual OTree* createWriter(const std::string& format) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:51:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ITree* IOTreeFactory::createReader(const std::string& format) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTreeFactory.cpp:59:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
OTree* IOTreeFactory::createWriter(const std::string& format) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:69:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node> * Newick::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:96:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:113:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:129:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::read(istream& in, vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:155:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.cpp:175:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Newick::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:92:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:97:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:105:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:109:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:120:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:124:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:132:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:136:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:143:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:146:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:148:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.h:151:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:75:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node> * NexusIOTree::read(istream &in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:88:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:167:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:177:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:186:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/NexusIoTree.cpp:251:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NexusIOTree::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:99:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* Nhx::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:126:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const Tree& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:136:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const TreeTemplate<N>& tree, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:145:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::read(istream& in, vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const vector<Tree*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:189:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Nhx::write_(const vector<TreeTemplate<N>*>& trees, ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:201:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Nhx::Element Nhx::getElement(const string& elt) const throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:329:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* Nhx::parenthesisToTree(const string& description) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:348:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string Nhx::propertyToString_(const Clonable* pptObject, short type) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.cpp:381:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* Nhx::stringToProperty_(const string& pptDesc, short type) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:148:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:173:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::setSubstitutionModel(TransitionModel* model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:238:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:287:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::applyParameters() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:86:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:94:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:117:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:125:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:139:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:146:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual DistanceMatrix* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:160:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoDistanceMatrix.h:167:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:70:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:74:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:76:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h:80:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const DistanceMatrix& dist, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:56:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
DistanceMatrix * PhylipDistanceMatrixFormat::read(istream& in) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp:96:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PhylipDistanceMatrixFormat::write(const DistanceMatrix& dist, ostream& out) const throw (Exception)
^~~~~
[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:64:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:195:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:314:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::applyParameters() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:65:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:148:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:173:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::setSubstitutionModel(TransitionModel* model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:238:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:287:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractHomogeneousTreeLikelihood::applyParameters() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:51:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:104:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:210:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::reInit() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:215:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::reInit(const Node* node) throw (Exception)
^~~~~
[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:64:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:168:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:195:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:314:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractNonHomogeneousTreeLikelihood::applyParameters() throw (Exception)
^~~~~
[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)':
/usr/include/c++/7/bits/stl_vector.h:1210:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
^
/usr/include/c++/7/bits/stl_vector.h:1210:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
^
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:95:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:193:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SitePatterns* DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception)
^~~~~
[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:98:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:124:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:145:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:167:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:175:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:181:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:60:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool rootArray) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:88:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:151:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:162:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:401:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:465:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:51:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:104:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:210:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::reInit() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:215:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASDRTreeLikelihoodData::reInit(const Node* node) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::DRASDRTreeLikelihoodData::reInit(const bpp::Node*)':
/usr/include/c++/7/bits/stl_vector.h:1210:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
^
/usr/include/c++/7/bits/stl_vector.h:1210:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
^
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:56:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:95:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRASRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:193:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SitePatterns* DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:83:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:94:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousTreeLikelihood::init_() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:234:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:281:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:345:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:431:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:120:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:138:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:149:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:154:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:182:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:187:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:194:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:202:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:203:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:85:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:98:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRNonHomogeneousTreeLikelihood::init_() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:238:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:306:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:374:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:503:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:98:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:124:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:145:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:167:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:175:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:181:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:60:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool rootArray) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:88:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:151:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:162:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:401:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:465:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(const bpp::DRHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:83:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:94:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousTreeLikelihood::init_() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:135:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:234:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:281:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:345:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:431:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:120:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:138:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:149:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:154:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:182:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:187:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:194:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:202:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:203:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:66:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:85:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:98:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRNonHomogeneousTreeLikelihood::init_() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:238:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:306:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:374:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:503:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:76:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& pl) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:81:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return tl_->getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:89:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return tl_->getSecondOrderDerivative(variable1, variable2); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:90:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getSecondOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getFirstOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:106:138: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception)
^~~~~
[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const bpp::Node*&&>, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair<const bpp::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<const bpp::Node* const, double> >; _Compare = std::less<const bpp::Node*>; _Alloc = std::allocator<std::pair<const bpp::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In member function 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()':
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:130:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:153:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:207:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double NNIHomogeneousTreeLikelihood::testNNI(int nodeId) const throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:314:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNIHomogeneousTreeLikelihood::doNNI(int nodeId) throw (NodeException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:81:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:95:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& modelName = "") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:104:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModel(const bpp::TreeLikelihood& treelikelihood) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:113:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModels(const PairedSiteLikelihoods& psl) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:141:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::size_t getNumberOfSites() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:63:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<string>& modelNames) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:90:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:99:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PairedSiteLikelihoods::appendModel(const bpp::TreeLikelihood& treeLikelihood) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:107:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PairedSiteLikelihoods::appendModels(const PairedSiteLikelihoods& psl) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'void bpp::BranchLikelihood::computeLogLikelihood()':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:76:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& pl) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:81:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return tl_->getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:89:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return tl_->getSecondOrderDerivative(variable1, variable2); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:90:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getSecondOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getFirstOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:106:138: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:130:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:153:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:207:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double NNIHomogeneousTreeLikelihood::testNNI(int nodeId) const throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:314:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNIHomogeneousTreeLikelihood::doNNI(int nodeId) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:86:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PseudoNewtonOptimizer::doInit(const ParameterList& params) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:96:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double PseudoNewtonOptimizer::doStep() throw (Exception)
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const bpp::Node*&&>, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair<const bpp::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<const bpp::Node* const, double> >; _Compare = std::less<const bpp::Node*>; _Alloc = std::allocator<std::pair<const bpp::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40:
/usr/include/c++/7/bits/stl_map.h: In member function 'void bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_()':
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:81:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:95:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::string& modelName = "") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:104:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModel(const bpp::TreeLikelihood& treelikelihood) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:113:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void appendModels(const PairedSiteLikelihoods& psl) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:141:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::size_t getNumberOfSites() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:63:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const vector<string>& modelNames) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:90:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:99:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PairedSiteLikelihoods::appendModel(const bpp::TreeLikelihood& treeLikelihood) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'void bpp::BranchLikelihood::computeLogLikelihood()':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:107:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PairedSiteLikelihoods::appendModels(const PairedSiteLikelihoods& psl) throw (Exception)
^~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:119:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:139:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:143:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getNonDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:144:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:145:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:146:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:161:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights(Node* node, double height) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:60:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:75:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:93:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousClockTreeLikelihood::applyParameters() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:163:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(Node* node, double height) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:185:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList RHomogeneousClockTreeLikelihood::getDerivableParameters() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:193:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList RHomogeneousClockTreeLikelihood::getNonDerivableParameters() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:204:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:214:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RASTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:86:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void PseudoNewtonOptimizer::doInit(const ParameterList& params) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:96:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double PseudoNewtonOptimizer::doStep() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:92:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:117:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:135:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:153:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:60:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool usePatterns) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:84:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool usePatterns) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:142:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:152:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const bpp::Node*&&>, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair<const bpp::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<const bpp::Node* const, double> >; _Compare = std::less<const bpp::Node*>; _Alloc = std::allocator<std::pair<const bpp::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)':
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:119:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:139:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:143:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getNonDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:144:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:145:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:146:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:161:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights(Node* node, double height) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:60:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:75:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception):
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:93:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousClockTreeLikelihood::applyParameters() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:163:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(Node* node, double height) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:185:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList RHomogeneousClockTreeLikelihood::getDerivableParameters() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:193:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList RHomogeneousClockTreeLikelihood::getNonDerivableParameters() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:204:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:214:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:92:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:117:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:135:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:153:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:60:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool usePatterns) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:84:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool usePatterns) throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:142:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:152:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:62:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:80:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:91:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousTreeLikelihood::init_(bool usePatterns) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:133:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:251:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:291:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:351:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:602:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const bpp::Node*&&>, std::tuple<>}; _Key = const bpp::Node*; _Val = std::pair<const bpp::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<const bpp::Node* const, double> >; _Compare = std::less<const bpp::Node*>; _Alloc = std::allocator<std::pair<const bpp::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Utils/MapTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(bool)':
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:512:4: note: parameter passing for argument of type 'std::_Rb_tree<const bpp::Node*, std::pair<const bpp::Node* const, double>, std::_Select1st<std::pair<const bpp::Node* const, double> >, std::less<const bpp::Node*>, std::allocator<std::pair<const bpp::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const bpp::Node* const, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:62:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:80:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:91:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousTreeLikelihood::init_(bool usePatterns) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:133:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:251:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:291:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:351:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:602:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(const bpp::RHomogeneousMixedTreeLikelihood&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:224:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:242:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:246:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:63:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:87:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:314:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:437:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:63:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:83:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:96:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousTreeLikelihood::init_(bool usePatterns) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:138:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:255:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:317:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:377:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:849:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::RHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:224:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:242:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:246:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:63:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:87:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:314:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousMixedTreeLikelihood::initialize() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:437:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousMixedTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:49:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:59:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:100:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:132:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void alphabetIndexHasChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:200:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionReward::alphabetIndexHasChanged() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:63:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:83:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:96:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousTreeLikelihood::init_(bool usePatterns) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:138:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void RNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:255:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:317:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:377:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:849:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:270:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionSubstitutionCount::substitutionRegisterHasChanged() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:288:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionSubstitutionCount::weightsHaveChanged() throw (Exception)
^~~~~
[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp
[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:49:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:59:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:100:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:132:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void alphabetIndexHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.cpp:200:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionReward::alphabetIndexHasChanged() throw (Exception)
^~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:55,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual double bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood() const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:270:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionSubstitutionCount::substitutionRegisterHasChanged() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:288:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DecompositionSubstitutionCount::weightsHaveChanged() throw (Exception)
^~~~~
[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp
[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:85:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:101:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:112:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:62:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:354:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:380:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:83:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:106:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:113:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:138:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:162:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:183:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:195:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:218:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:230:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:132:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void alphabetIndexHasChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:85:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:101:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:112:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:67:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:378:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:688:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:985:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1263:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1289:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Reward.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:85:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:101:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:112:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:62:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:354:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp:380:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:255:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void UniformizationSubstitutionCount::substitutionRegisterHasChanged() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:272:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void UniformizationSubstitutionCount::weightsHaveChanged() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:83:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:106:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:113:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:138:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:162:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:183:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:195:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:218:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:230:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:132:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void alphabetIndexHasChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:85:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:101:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/RewardMappingTools.h:112:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/DRTreeLikelihoodTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:80:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:98:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves = false) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Likelihood/TreeLikelihoodTools.h:112:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool alsoForLeaves) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:67:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:378:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:688:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:985:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1263:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:1289:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:255:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void UniformizationSubstitutionCount::substitutionRegisterHasChanged() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:272:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void UniformizationSubstitutionCount::weightsHaveChanged() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp
[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp
[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp
[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:354:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double AbstractSubstitutionModel::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'bpp::AbstractMixedSubstitutionModel& bpp::AbstractMixedSubstitutionModel::operator=(const bpp::AbstractMixedSubstitutionModel&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:354:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double AbstractSubstitutionModel::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp
[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp
[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp
[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp
[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp
[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp
[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp
[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp
[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp
[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp
[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp
[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp
[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/GY94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp
[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KCM.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp
[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp
[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/MG94.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::SENCA::setFreq(std::map<int, double>&)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:52,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h:43,
from /usr/include/Bpp/Seq/GeneticCode/GeneticCode.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/SENCA.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'virtual void bpp::SENCA::setFreq(std::map<int, double>&)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp
[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp
[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp
[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp
[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp
[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector<double, std::allocator<double> >&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp
[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp
[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:150:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet::FixedFrequenciesSet(StateMap* stateMap, const vector<double>& initFreqs, const string& name) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:88:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::updateFrequencies() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:131:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::setFrequencies(const vector<double>& frequencies) throw (DimensionException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:134:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:145:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception)
^~~~~
[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullCodonFrequenciesSet::FullCodonFrequenciesSet(const bpp::GeneticCode*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/WordAlphabet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::FullPerAACodonFrequenciesSet::setFrequencies(const std::vector<double, std::allocator<double> >&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:150:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet::FixedFrequenciesSet(StateMap* stateMap, const vector<double>& initFreqs, const string& name) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:99:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setFrequencies(const std::vector<double>& frequencies) throw (DimensionException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:103:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void updateFrequencies() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:107:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:108:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:109:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h:110:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:88:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::updateFrequencies() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:131:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::setFrequencies(const vector<double>& frequencies) throw (DimensionException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:134:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp:145:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void MvaFrequenciesSet::computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs) throw (Exception)
^~~~~
[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp
[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/../StateMap.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp:41:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In constructor 'bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::StateMap*, bool, short unsigned int, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp
[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:174:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h:174:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp
[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:202:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double MarkovModulatedSubstitutionModel::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:227:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:202:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double MarkovModulatedSubstitutionModel::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:56:12: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int tto) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h:115:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int ffrom = -1, int tto = -1) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp:56:12: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int tto) throw (Exception) :
^~~~~
[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp
[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/F84.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp
[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp
[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/K80.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/L95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp
[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp
[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp
[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:131:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:359:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp
[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp
[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp
[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:39:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.h:131:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp:359:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp
[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp
[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h:156:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/Coala.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47,
from /usr/include/Bpp/Numeric/Function/Functions.h:45,
from /usr/include/Bpp/Numeric/NumTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47,
from /usr/include/Bpp/Numeric/Function/Functions.h:45,
from /usr/include/Bpp/Numeric/NumTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp
[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp
In file included from /usr/include/c++/7/map:60:0,
from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47,
from /usr/include/Bpp/Numeric/Function/Functions.h:45,
from /usr/include/Bpp/Numeric/NumTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/DSO78.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /usr/include/c++/7/map:61:0,
from /usr/include/Bpp/Numeric/AbstractParametrizable.h:47,
from /usr/include/Bpp/Numeric/Function/Functions.h:45,
from /usr/include/Bpp/Numeric/NumTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/Matrix.h:48,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp:41:
/usr/include/c++/7/bits/stl_map.h: In member function 'bpp::ParameterList bpp::CoalaCore::computeCOA(const bpp::SequenceContainer&, bool)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JCprot.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/JTT92.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp
[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp
[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp
[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:297:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double RE08::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/StateMap.cpp
[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp
[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixedSubstitutionModel.h:42:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractMixedSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../MixtureOfSubstitutionModels.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioMixedSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:116:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:172:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SubstitutionModelSet::replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:253:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:268:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:284:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:52:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:87:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception)
^~~~~
[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:85:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::search() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchFast() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:149:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchBetter() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:214:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchPhyML() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:98:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Node::swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:130:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t Node::getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:146:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double Node::getBootstrapValue() const throw (PropertyNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:76:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& pl) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:81:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return tl_->getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:89:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return tl_->getSecondOrderDerivative(variable1, variable2); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:90:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getSecondOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getFirstOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:92:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:100:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:128:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:163:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:267:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:358:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:417:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:486:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:579:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:611:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:651:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:687:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:114:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:143:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(begin() + (__position - cbegin()), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp: In member function 'void bpp::NNITopologySearch::searchPhyML()':
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:290:31: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
improvement.insert(improvement.begin() + static_cast<ptrdiff_t>(pos), diff);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:296:31: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
improvement.insert(improvement.end(), diff);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::NNITopologySearch::searchBetter()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:54:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:72:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractTreeParsimonyScore::init_(const SiteContainer& data, bool verbose) throw (Exception)
^~~~~
[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/WAG01.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Protein/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.h:193:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/RE08.cpp:297:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double RE08::getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException)
^~~~~
[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/StateMap.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:90:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:112:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:178:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::reInit() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:184:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::reInit(const Node* node) throw (Exception)
^~~~~
[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp
[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:57:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:70:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:313:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double DRTreeParsimonyScore::testNNI(int nodeId) const throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:385:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyScore::doNNI(int nodeId) throw (NodeException)
^~~~~
[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:116:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:172:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void SubstitutionModelSet::replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:253:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:268:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp:284:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:52:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp:87:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:59:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:74:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::getSequenceSubset(const SiteContainer& sequenceSet, const vector<string>& names) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:88:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::shrinkSiteSet(const SiteContainer& siteSet) throw (Exception)
^~~~~
[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp
[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp:39:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:85:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::search() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:97:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchFast() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:149:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchBetter() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:214:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void NNITopologySearch::searchPhyML() throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:98:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void Node::swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:130:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t Node::getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.cpp:146:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double Node::getBootstrapValue() const throw (PropertyNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.h:108:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:70:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:94:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:60:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Tree* tree) throw (Exception) :
^~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:114:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:143:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(begin() + (__position - cbegin()), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp: In member function 'void bpp::NNITopologySearch::searchPhyML()':
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:290:31: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
improvement.insert(improvement.begin() + static_cast<ptrdiff_t>(pos), diff);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:296:31: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
improvement.insert(improvement.end(), diff);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::NNITopologySearch::searchBetter()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:76:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& pl) throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:81:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return tl_->getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:89:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return tl_->getSecondOrderDerivative(variable1, variable2); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:90:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getSecondOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:91:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception) { return tl_->getFirstOrderDerivative(variable); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:97:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights_(const Node* node, double height, ParameterList& brlenPl) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:92:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:100:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:128:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:163:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:267:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:358:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:417:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:486:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:579:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:611:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:651:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.cpp:687:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose) throw (Exception)
^~~~~
[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:54:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:72:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp:82:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void AbstractTreeParsimonyScore::init_(const SiteContainer& data, bool verbose) throw (Exception)
^~~~~
[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/SymbolList.h:43,
from /usr/include/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SiteSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator<bpp::MutationPath>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<bpp::MutationPath>::iterator {aka __gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/SymbolList.h:43,
from /usr/include/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SiteSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:90:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:112:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:178:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::reInit() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp:184:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyData::reInit(const Node* node) throw (Exception)
^~~~~
[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp
[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:190:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplateTools::Element TreeTemplateTools::getElement(const string& elt) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:335:156: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* TreeTemplateTools::parenthesisToTree(const string& description, bool bootstrap, const string& propertyName, bool withId, bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:508:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Vdouble TreeTemplateTools::getBranchLengths(const Node& node) throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:525:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTemplateTools::getTotalLength(const Node& node, bool includeAncestor) throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:573:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTemplateTools::scaleTree(Node& node, double factor) throw (NodePException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:83:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:101:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:106:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeTree() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:76:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:83:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:98:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:119:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:134:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:153:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:160:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::getNodesId(const Tree& tree, int nodeId, vector<int>& nodes) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:174:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:191:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getDepths(const Tree& tree, int nodeId, map<int, size_t>& depths) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:209:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:231:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getHeights(const Tree& tree, int nodeId, map<int, double>& heights) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:254:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string TreeTools::nodeToParenthesis(const Tree& tree, int nodeId, bool writeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:292:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string TreeTools::nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const string& propertyName) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:402:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:472:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Vdouble TreeTools::getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:495:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getTotalLength(const Tree& tree, int nodeId, bool includeAncestor) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:512:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:525:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:539:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:558:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:590:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:619:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:783:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool TreeTools::checkIds(const Tree& tree, bool throwException) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:892:132: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int TreeTools::robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames, int* missing_in_tr2, int* missing_in_tr1) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1022:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* TreeTools::thresholdConsensus(const vector<Tree*>& vecTr, double threshold, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1158:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1172:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int TreeTools::getLastCommonAncestor(const Tree& tree, const vector<int>& nodeIds) throw (NodeNotFoundException, Exception)
^~~~~
[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp
[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:57:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:70:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:313:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double DRTreeParsimonyScore::testNNI(int nodeId) const throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp:385:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void DRTreeParsimonyScore::doNNI(int nodeId) throw (NodeException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:59:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:74:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::getSequenceSubset(const SiteContainer& sequenceSet, const vector<string>& names) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/PatternTools.cpp:88:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SiteContainer* PatternTools::shrinkSiteSet(const SiteContainer& siteSet) throw (Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, double> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:41:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTools::getBranchLengths(const bpp::Tree&, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/PhyloStatistics.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void bpp::PhyloStatistics::computeForSubtree_(const bpp::Node*, double&, size_t&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/SubstitutionRegister.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/MutationProcess.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Mapping/../Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
[ 90%] Linking CXX static library libbpp-phyl.a
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-phyl-static.dir/cmake_clean_target.cmake
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-static.dir/link.txt --verbose=1
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/usr/bin/ar qc libbpp-phyl.a CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:60:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Tree* tree) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.h:108:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:70:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp:94:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception)
^~~~~
/usr/bin/ranlib libbpp-phyl.a
[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.cpp
[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 91%] Built target bpp-phyl-static
[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/SitePatterns.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:190:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplateTools::Element TreeTemplateTools::getElement(const string& elt) throw (IOException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:335:156: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* TreeTemplateTools::parenthesisToTree(const string& description, bool bootstrap, const string& propertyName, bool withId, bool verbose) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:508:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Vdouble TreeTemplateTools::getBranchLengths(const Node& node) throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:525:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTemplateTools::getTotalLength(const Node& node, bool includeAncestor) throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:573:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTemplateTools::scaleTree(Node& node, double factor) throw (NodePException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:142:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* mergeBipartitionLists(const std::vector<BipartitionList*>& vecBipartL, bool checkElements = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:147:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static BipartitionList* buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:166:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncode(const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionTools.h:175:171: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static VectorSiteContainer* MRPEncodeMultilabel( const std::vector<BipartitionList*>& vecBipartL) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:114:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:142:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void computeTree() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:163:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:84:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NeighborJoining(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:100:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/NeighborJoining.h:109:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<size_t> getBestPair() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:83:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false, bool verbose = true) throw (Exception) :
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:101:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/BioNJ.h:106:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeTree() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:76:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:83:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:98:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:119:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:134:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:153:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:160:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::getNodesId(const Tree& tree, int nodeId, vector<int>& nodes) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:174:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:191:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::getDepths(const Tree& tree, int nodeId, map<int, size_t>& depths) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:209:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:231:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getHeights(const Tree& tree, int nodeId, map<int, double>& heights) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:254:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string TreeTools::nodeToParenthesis(const Tree& tree, int nodeId, bool writeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:292:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
string TreeTools::nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const string& propertyName) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:402:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:472:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Vdouble TreeTools::getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:495:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double TreeTools::getTotalLength(const Tree& tree, int nodeId, bool includeAncestor) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:512:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:525:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:539:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void TreeTools::scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:558:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t TreeTools::initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:590:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeNotFoundException, NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:619:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:783:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool TreeTools::checkIds(const Tree& tree, bool throwException) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:892:132: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int TreeTools::robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames, int* missing_in_tr2, int* missing_in_tr1) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1022:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* TreeTools::thresholdConsensus(const vector<Tree*>& vecTr, double threshold, bool checkNames) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1158:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
vector<int> TreeTools::getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:1172:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int TreeTools::getLastCommonAncestor(const Tree& tree, const vector<int>& nodeIds) throw (NodeNotFoundException, Exception)
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/SymbolList.h:43,
from /usr/include/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SiteSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator<bpp::MutationPath>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<bpp::MutationPath>::iterator {aka __gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45,
from /usr/include/Bpp/Seq/SymbolList.h:43,
from /usr/include/Bpp/Seq/Site.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/SiteSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp:42:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTemplateTools::getBranchLengths(const bpp::Node&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.cpp:42:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, double> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double>}; _Tp = std::pair<std::__cxx11::basic_string<char>, double>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, double>*, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeExceptions.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bpp::Vdouble bpp::TreeTools::getBranchLengths(const bpp::Tree&, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 92%] Linking CXX shared library libbpp-phyl.so
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-shared.dir/link.txt --verbose=1
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CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl.so.11.0.0 libbpp-phyl.so.11 libbpp-phyl.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_clock.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_nh.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_mapping.dir/DependInfo.cmake --color=
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[ 92%] Building CXX object test/CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.cpp.o -c /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp
[ 93%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o
[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /<<PKGBUILDDIR>>/test/test_mapping.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp
[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /<<PKGBUILDDIR>>/test/test_likelihood.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:45:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:46:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:94:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:119:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:139:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:142:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:143:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ParameterList getNonDerivableParameters() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:144:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:145:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:146:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:161:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeBranchLengthsFromHeights(Node* node, double height) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:97:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:120:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:138:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:149:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:154:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:182:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:187:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:194:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:202:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:203:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:115:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:140:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:155:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:166:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:198:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:199:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:201:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:54:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionReward.h:132:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void alphabetIndexHasChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:58:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:58:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:59:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:59:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:83:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:106:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:113:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:138:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:162:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:183:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:195:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:218:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping.cpp:59:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:230:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 94%] Linking CXX executable test_likelihood_clock
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 94%] Built target test_likelihood_clock
make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_simulations.dir/DependInfo.cmake --color=
Scanning dependencies of target test_simulations
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /<<PKGBUILDDIR>>/test/test_simulations.cpp
[ 95%] Linking CXX executable test_likelihood
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Built target test_likelihood
make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake --color=
Scanning dependencies of target test_detailed_simulations
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator<bpp::MutationPath>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<bpp::MutationPath>::iterator {aka __gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
[ 95%] Linking CXX executable test_likelihood_nh
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_nh.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_nh.dir/test_likelihood_nh.cpp.o -o test_likelihood_nh -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
[ 95%] Built target test_likelihood_nh
make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
In file included from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_mapping_codon.dir/DependInfo.cmake --color=
In file included from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
Scanning dependencies of target test_mapping_codon
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:45:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 95%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:264:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:281:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initLikelihoods(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:46:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:299:135: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual SitePatterns* initLikelihoodsWithPatterns(const Node* node, const SiteContainer& sequences, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:46:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:49:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:117:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:141:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:156:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(bool usePatterns) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:167:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:172:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:200:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:201:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:208:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:216:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:217:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (ParameterNotFoundException, ConstraintException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return lnL_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getValue(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void search() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchFast() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchBetter() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void searchPhyML() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFunctionValue() const throw (NullPointerException) { return currentValue_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doInit(const ParameterList& params) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double doStep() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeLikelihoodData* getLikelihoodData() const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return rootPatternLinks_[site]; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer& sites) throw (Exception) {}
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const throw (NotImplementedException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initTreeLikelihoods(const SequenceContainer & sequences) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void computeMatrix() throw (NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel& getSubstitutionModel() const throw (Exception) {
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const DiscreteDistribution& getRateDistribution() const throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void optimizationStepPerformed(const OptimizationEvent &event) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_simulations.cpp:50:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& lambda) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (ParameterException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const ParameterList& getParameters() const throw (Exception) { return lambda_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Parameter& getParameter(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getParameterValue(const std::string& name) const throw (ParameterNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
unsigned int verbose = 0) throw (Exception);
^~~~~
[ 95%] Linking CXX executable test_mapping
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Built target test_mapping
make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_models.dir/DependInfo.cmake --color=
Scanning dependencies of target test_models
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_models.dir/test_models.cpp.o -c /<<PKGBUILDDIR>>/test/test_models.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:49:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:52:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:82:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:103:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:133:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstBranchModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual ConstSiteModelDescription* next() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:194:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void initialize() throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:357:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:368:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:392:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:91:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:122:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:181:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstNoPartitionBranchModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:302:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception) { initialized_ = true; }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:67:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:66:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:71:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h:90:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModel(TransitionModel* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:74:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:125:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:151:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:169:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:204:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:207:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) { return model_; }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:209:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModel(TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:226:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:230:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:240:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:68:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:73:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:85:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:94:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:110:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSubstitutionModelSet(SubstitutionModelSet* model) throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:81:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
ConstSiteModelDescription* next() throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:139:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:166:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:185:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initialize() throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:196:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getSubstitutionModelForNode(int nodeId) const throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:201:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getSubstitutionModelForNode(int nodeId) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:233:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionModelSet(SubstitutionModelSet* modelSet) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:254:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void applyParameters() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:258:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMinimumBranchLength(double minimum) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:268:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setMaximumBranchLength(double maximum) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:74:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const Node& node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:83:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* getSequenceSubset(const SiteContainer& sequenceSet, const std::vector<std::string>& names) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../PatternTools.h:91:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static SiteContainer* shrinkSiteSet(const SiteContainer& sequenceSet) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:407:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:416:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:418:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:437:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void initLikelihoods(const Node* node, const SiteContainer& sites, const TransitionModel& model) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setData(const SiteContainer & sites) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:53:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList & parameters) throw (ParameterNotFoundException, ConstraintException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:55:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:171:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:56:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:57:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:117:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:118:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:58:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:127:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void substitutionRegisterHasChanged() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:128:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void weightsHaveChanged() throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:59:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:106:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:59:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:178:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TreeTemplate<Node>& getTree() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getSitePosition(size_t index) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:198:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSitePosition(size_t index, int position) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/Mapping.h:226:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getNodeIndex(int nodeId) const throw (NodeNotFoundException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:45:0,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:60:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:110:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setSubstitutionRegister(SubstitutionRegister* reg) throw (Exception) {
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:83:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:106:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:113:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:138:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:162:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:183:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:195:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool verbose = true) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:218:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:60:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:230:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (IOException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43:0,
from /<<PKGBUILDDIR>>/test/test_models.cpp:41:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (BadIntException) { return getModel().getInitValue(i, state); }
^~~~~
/<<PKGBUILDDIR>>/test/test_models.cpp:69:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setParameters(const ParameterList& pl) throw (bpp::ParameterNotFoundException
^~~~~
/<<PKGBUILDDIR>>/test/test_models.cpp:74:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getValue() const throw (Exception) { return 0; }
^~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 95%] Linking CXX executable test_models
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Built target test_models
make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_nhx.dir/DependInfo.cmake --color=
Scanning dependencies of target test_nhx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /<<PKGBUILDDIR>>/test/test_nhx.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator<bpp::MutationPath>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<bpp::MutationPath>::iterator {aka __gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h:43,
from /usr/include/Bpp/Numeric/Prob/ConstantDistribution.h:43,
from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_nhx.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:43:0,
from /<<PKGBUILDDIR>>/test/test_nhx.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_nhx.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:170:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:175:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:183:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:188:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:199:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:203:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:211:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:215:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:221:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* parenthesisToTree(const std::string& description) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:255:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:258:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:260:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:263:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:265:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Element getElement(const std::string& elt) const throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:277:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string propertyToString_(const Clonable* pptObject, short type) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Nhx.h:278:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Clonable* stringToProperty_(const std::string& pptDesc, short type) throw (Exception);
^~~~~
[ 96%] Linking CXX executable test_detailed_simulations
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Built target test_detailed_simulations
make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_bowker.dir/DependInfo.cmake --color=
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
Scanning dependencies of target test_bowker
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /<<PKGBUILDDIR>>/test/test_bowker.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Io/FileTools.h:46,
from /usr/include/Bpp/App/ApplicationTools.h:44,
from /<<PKGBUILDDIR>>/test/test_mapping_codon.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const bpp::MutationPath&}; _Tp = bpp::MutationPath; _Alloc = std::allocator<bpp::MutationPath>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<bpp::MutationPath>::iterator {aka __gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Exceptions.h:46,
from /usr/include/Bpp/Numeric/VectorExceptions.h:43,
from /usr/include/Bpp/Numeric/VectorTools.h:43,
from /usr/include/Bpp/Numeric/Matrix/MatrixTools.h:43,
from /<<PKGBUILDDIR>>/test/test_simulations.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void bpp::SiteSimulationResult::addNode(int, bpp::MutationPath)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bpp::MutationPath*, std::vector<bpp::MutationPath> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'int main()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/T92.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);
^~~~~
[ 97%] Linking CXX executable test_nhx
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:43:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:47:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:221:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getNumberOfStates() const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:250:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:257:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:264:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getTransitionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:270:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getTransitionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:281:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:294:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModel(size_t i) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:327:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getModelIndexForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:342:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:349:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TransitionModel* getModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:357:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:362:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:374:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:386:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:416:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void replaceModel(size_t modelIndex, TransitionModel* model) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:528:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:551:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanModels(bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:553:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSet.h:555:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_bowker.cpp:47:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:74:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h:95:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (AlphabetException, Exception);
^~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Built target test_nhx
make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake --color=
Scanning dependencies of target test_parsimony
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /<<PKGBUILDDIR>>/test/test_parsimony.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:47:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:147:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const NodeTemplate<NodeInfos>* getSon(size_t i) const throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../NodeTemplate.h:149:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
NodeTemplate<NodeInfos>* getSon(size_t i) throw (IndexOutOfBoundsException) { return dynamic_cast<NodeTemplate<NodeInfos> *>(sons_[i]); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:48:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
) throw (Exception);
^~~~~
[ 97%] Linking CXX executable test_simulations
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Built target test_simulations
make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree.dir/DependInfo.cmake --color=
Scanning dependencies of target test_tree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o
[ 98%] Linking CXX executable test_mapping_codon
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /<<PKGBUILDDIR>>/test/test_tree.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 98%] Built target test_mapping_codon
make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake --color=
Scanning dependencies of target test_tree_getpath
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp
In file included from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:44:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:43:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init_(const SiteContainer& data, bool verbose) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit() throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void init(const Node* node, const SiteContainer& sites, const StateMap& stateMap) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void reInit(const Node* node) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void search() throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double testNNI(int nodeId) const throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void doNNI(int nodeId) throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTopologyValue() const throw (Exception) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTopologyValue() const throw (Exception) { return getScore(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double testNNI(int nodeId) const throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void doNNI(int nodeId) throw (NodeException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
from /<<PKGBUILDDIR>>/test/test_tree.cpp:42:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(std::istream& in) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Tree* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:42:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const Tree& tree, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite = true) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const Tree& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream& out) const throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree_getpath.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
[ 99%] Linking CXX executable test_tree_getpath
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_getpath.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -o test_tree_getpath -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Built target test_tree_getpath
make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake --color=
Scanning dependencies of target test_tree_rootat
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:236:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getName() const throw (NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:355:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setFather(Node* node) throw (NullPointerException)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:44:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:395:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Node* getSon(size_t pos) const throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:401:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* getSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:407:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(size_t pos, Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:419:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void addSon(Node* node) throw (NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:430:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setSon(size_t pos, Node* node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:444:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Node* removeSon(size_t pos) throw (IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:454:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void removeSon(Node* node) throw (NodeNotFoundException, NullPointerException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:476:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void swap(size_t branch1, size_t branch2) throw (IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:478:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual size_t getSonPosition(const Node* son) const throw (NodeNotFoundException, NullPointerException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:527:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:535:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:543:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:555:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:617:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:625:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(const std::string& name) const throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:633:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:645:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteBranchProperty(const std::string& name) throw (PropertyNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Node.h:684:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getBootstrapValue() const throw (PropertyNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:192:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getLeafId(const std::string& name) const throw (NodeNotFoundException)= 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:202:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:204:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:206:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual int getFatherId(int parentId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:208:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasFather(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:217:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::string getNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:219:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:221:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void deleteNodeName(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:223:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeName(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:233:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isLeaf(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:235:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool isRoot(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:254:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(const Tree& tree, int nodeId, size_t i1 = 0, size_t i2 = 1) throw (NodeNotFoundException,IndexOutOfBoundsException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:277:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:279:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:281:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:283:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:285:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:287:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:295:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:297:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void setBranchProperty(int nodeId, const std::string& name, const Clonable & property) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:299:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:301:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:303:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:305:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:316:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void rootAt(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:327:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void newOutGroup(int nodeId) throw (NodeNotFoundException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:342:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual bool unroot() throw (UnrootedTreeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:364:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual std::vector<double> getBranchLengths() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:372:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual double getTotalLength() throw (NodeException) = 0;
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Tree.h:396:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual void scaleTree(double factor) throw (NodeException) = 0;
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:46:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:135:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::map<std::string, bool> getBipartition(size_t i) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:137:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int* getBitBipartition(size_t i) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:141:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:143:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteBipartition(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:149:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:151:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areIdentical(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:163:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areCompatible(size_t k1, size_t k2) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:176:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:192:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void flip(size_t i) throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:197:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
size_t getPartitionSize(size_t i) const throw(Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/BipartitionList.h:207:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
TreeTemplate<Node>* toTree() const throw(Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>& leaves) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Tree& tree, int nodeId, const std::string& name) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Tree& tree, int nodeId, const std::string& name, int*& id) throw (NodeNotFoundException);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int nodeId1, int nodeId2, bool includeAncestor = true) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLastCommonAncestor(const Tree& tree, const std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepth(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t getDepths(const Tree& tree, int nodeId, std::map<int, size_t>& depths) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeight(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getHeights(const Tree& tree, int nodeId, std::map<int, double>& heights) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Tree& tree, int nodeId, bool includeAncestor = true) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Tree& tree, int nodeId, double factor) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, double power = 1, bool init = true) throw (NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double power, double total, double& height, double& heightRaised) throw (NodeNotFoundException,NodeException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool writeId = false) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void getNodesId(const Tree& tree, int nodeId, std::vector<int>& nodes) throw (NodeNotFoundException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static bool checkIds(const Tree& tree, bool throwException) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL) throw (Exception);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>& vecTr, double threshold, bool checkNames = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static int getLeafId(const Node& node, const std::string& name) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void searchLeaf(const Node& node, const std::string& name, int*& id) throw (NodeNotFoundException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw (Exception)
^~~~~
In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Vdouble getBranchLengths(const Node& node) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static double getTotalLength(const Node& node, bool includeAncestor = true) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static void scaleTree(Node& node, double factor) throw (NodePException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static Element getElement(const std::string& elt) throw (IOException);
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
static TreeTemplate<Node>* parenthesisToTree(const std::string& description, bool bootstrap = true, const std::string& propertyName = TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw (Exception);
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getLeafId(const std::string& name) const throw (NodeNotFoundException) { return TreeTemplateTools::getLeafId(*root_, name); }
^~~~~
In file included from /<<PKGBUILDDIR>>/test/test_tree_rootat.cpp:40:0:
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getSonsId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<int> getAncestorsId(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
int getFatherId(int parentId) const throw (NodeNotFoundException) { return getNode(parentId)->getFatherId(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasFather(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasFather(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::string getNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->hasName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeName(int nodeId, const std::string& name) throw (NodeNotFoundException) { getNode(nodeId)->setName(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return getNode(nodeId)->deleteName(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->isLeaf(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool isRoot(int nodeId) const throw (NodeNotFoundException) { return TreeTemplateTools::isRoot(*getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setNodeProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setNodeProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getNodeProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeNodeProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getNodePropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool hasBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void setBranchProperty(int nodeId, const std::string& name, const Clonable& property) throw (NodeNotFoundException) { getNode(nodeId)->setBranchProperty(name, property); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* getBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
const Clonable* getBranchProperty(int nodeId, const std::string& name) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
Clonable* removeBranchProperty(int nodeId, const std::string& name) throw (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<std::string> getBranchPropertyNames(int nodeId) const throw (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void rootAt(int nodeId) throw (NodeNotFoundException) { rootAt(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void newOutGroup(int nodeId) throw (NodeNotFoundException) { newOutGroup(getNode(nodeId)); }
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
bool unroot() throw (UnrootedTreeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
std::vector<double> getBranchLengths() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
double getTotalLength() throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void scaleTree(double factor) throw (NodeException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
void swapNodes(int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(int id, bool checkId = false) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(int id, bool checkId = false) const throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual N* getNode(const std::string& name) throw (NodeNotFoundException, Exception)
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
virtual const N* getNode(const std::string& name) const throw (NodeNotFoundException, Exception)
^~~~~
[ 99%] Linking CXX executable test_parsimony
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Built target test_parsimony
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h:45,
from /usr/include/Bpp/Seq/Alphabet/DNA.h:44,
from /<<PKGBUILDDIR>>/test/test_bowker.cpp:40:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::NodeTemplate<bpp::SimData>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 99%] Linking CXX executable test_tree
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
[100%] Linking CXX executable test_tree_rootat
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_rootat.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target test_tree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target test_tree_rootat
[100%] Linking CXX executable test_bowker
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src ../src/libbpp-phyl.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.11.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.3.0.0
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target test_bowker
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_auto_test -a
make -j4 test ARGS\+=-j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
Start 1: test_bowker
Start 2: test_detailed_simulations
Start 3: test_likelihood
Start 4: test_likelihood_clock
1/14 Test #4: test_likelihood_clock ............ Passed 0.61 sec
Start 5: test_likelihood_nh
2/14 Test #3: test_likelihood .................. Passed 1.13 sec
Start 6: test_mapping
3/14 Test #2: test_detailed_simulations ........ Passed 10.16 sec
Start 7: test_mapping_codon
4/14 Test #6: test_mapping ..................... Passed 14.36 sec
Start 8: test_models
5/14 Test #8: test_models ...................... Passed 0.71 sec
Start 9: test_nhx
6/14 Test #9: test_nhx ......................... Passed 0.31 sec
Start 10: test_parsimony
7/14 Test #10: test_parsimony ................... Passed 0.31 sec
Start 11: test_simulations
8/14 Test #11: test_simulations ................. Passed 105.88 sec
Start 12: test_tree
9/14 Test #1: test_bowker ...................... Passed 133.86 sec
Start 13: test_tree_getpath
10/14 Test #13: test_tree_getpath ................ Passed 0.31 sec
Start 14: test_tree_rootat
11/14 Test #14: test_tree_rootat ................. Passed 0.79 sec
12/14 Test #7: test_mapping_codon ............... Passed 128.20 sec
13/14 Test #12: test_tree ........................ Passed 44.84 sec
14/14 Test #5: test_likelihood_nh ............... Passed 1141.01 sec
100% tests passed, 0 tests failed out of 14
Total Test time (real) = 1141.83 sec
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend
make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build
make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/CMakeFiles/bpp-phyl-static.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 50%] Built target bpp-phyl-static
[ 92%] Built target bpp-phyl-shared
make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend
make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/depend
make -f test/CMakeFiles/test_likelihood_nh.dir/build.make test/CMakeFiles/test_likelihood_nh.dir/depend
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_mapping.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_nh.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_likelihood_clock.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build
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make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood_nh.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Nothing to be done for 'test/CMakeFiles/test_likelihood.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 92%] Built target test_likelihood
[ 92%] Built target test_likelihood_nh
[ 93%] Built target test_mapping
make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend
make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/depend
make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_simulations.dir/DependInfo.cmake --color=
[ 94%] Built target test_likelihood_clock
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake --color=
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make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-config.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-config-version.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.a
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11.0.0
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/AncestralStateReconstruction.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/App
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RASTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionReward.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/Mapping.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/Reward.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/MG94.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M2.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeTransitionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/CoalaCore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JCprot.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/NNITopologySearch.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Node.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/OptimizationTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/Tree.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets-none.cmake
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--override 's/libbpp-\([-a-z]\+\)[0-9]*-dev/libbpp-\1-dev/' \
--exclude-la \
--movedev debian/tmp/usr/include/* usr/include \
--movedev debian/tmp/usr/lib/*/cmake usr/lib/arm-linux-gnueabihf \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
--> libbpp-core-dev package exists.
--> libbpp-seq-dev package exists.
set -e
install -d -m 755 debian/libbpp-phyl-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libbpp-phyl11/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.a debian/libbpp-phyl-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so debian/libbpp-phyl-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11 debian/libbpp-phyl11/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11.0.0 debian/libbpp-phyl11/usr/lib/arm-linux-gnueabihf
PKGDEV=libbpp-phyl-dev
PKGSHL=libbpp-phyl11
install -d -m 755 debian/libbpp-phyl-dev/usr/include
mv debian/tmp/usr/include/Bpp debian/libbpp-phyl-dev/usr/include
install -d -m 755 debian/libbpp-phyl-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/cmake debian/libbpp-phyl-dev/usr/lib/arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libbpp-phyl11/usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11.0.0 found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package libbpp-phyl-dev: unused substitution variable ${devlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.3.1-10_armhf.deb'.
dpkg-deb: building package 'libbpp-phyl11-dbgsym' in '../libbpp-phyl11-dbgsym_2.3.1-10_armhf.deb'.
dpkg-deb: building package 'libbpp-phyl11' in '../libbpp-phyl11_2.3.1-10_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../libbpp-phyl_2.3.1-10_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build libbpp-phyl-2.3.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-08-31T16:44:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libbpp-phyl_2.3.1-10_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 23 Aug 2017 23:32:26 +0200
Source: libbpp-phyl
Binary: libbpp-phyl-dev libbpp-phyl11
Architecture: armhf
Version: 2.3.1-10
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libbpp-phyl-dev - Bio++ Phylogenetic library development files
libbpp-phyl11 - Bio++ Phylogenetic library
Closes: 871085
Changes:
libbpp-phyl (2.3.1-10) unstable; urgency=medium
.
[ Julien Dutheil ]
* Does not override debian cxx flags anymore.
.
[ Andreas Tille ]
* Rebuild with gcc-7
Closes: #871085
* Standards-Version: 4.0.1
* Fix d-shlibs override
Checksums-Sha1:
01308f6d20b7253c7e857dab7dd090581eeac87e 2782632 libbpp-phyl-dev_2.3.1-10_armhf.deb
c3f91d861a649bf53ce931d80464da06c50b28e3 29496384 libbpp-phyl11-dbgsym_2.3.1-10_armhf.deb
6bb513a0f3d27bff8951757ddc5b2292307a9859 1230092 libbpp-phyl11_2.3.1-10_armhf.deb
feee8837f580c84d4703c8ff893cfbe1d2dd64b4 6230 libbpp-phyl_2.3.1-10_armhf.buildinfo
Checksums-Sha256:
cb4fcea0816925c436d0ad80f74efcf2439f72de549edd52929535353690a399 2782632 libbpp-phyl-dev_2.3.1-10_armhf.deb
7e7b1f01f522ffa19f3d02874b2deae6aa3d202f314b20545cf3c997348c141c 29496384 libbpp-phyl11-dbgsym_2.3.1-10_armhf.deb
28e3f229fbea34a934865974c2067ea99d0a53d098e6bb7402c11f489fdf2dfb 1230092 libbpp-phyl11_2.3.1-10_armhf.deb
8409dacf6501db635d728fe8cd0b32e481869d97404b4c59bef85f0192782aff 6230 libbpp-phyl_2.3.1-10_armhf.buildinfo
Files:
3791e40733a0753d49590ead61aa34a5 2782632 libdevel optional libbpp-phyl-dev_2.3.1-10_armhf.deb
9b9cf521cb300a43c3981a85de2e9a74 29496384 debug extra libbpp-phyl11-dbgsym_2.3.1-10_armhf.deb
f2559f725305a264b29b37d5d70472b3 1230092 libs optional libbpp-phyl11_2.3.1-10_armhf.deb
3a2bc4137a0bcf9189ee62a4b5da4e78 6230 science optional libbpp-phyl_2.3.1-10_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libbpp-phyl-dev_2.3.1-10_armhf.deb
----------------------------------
new debian package, version 2.0.
size 2782632 bytes: control archive=7072 bytes.
868 bytes, 19 lines control
18881 bytes, 216 lines md5sums
Package: libbpp-phyl-dev
Source: libbpp-phyl
Version: 2.3.1-10
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 30527
Depends: libbpp-phyl11 (= 2.3.1-10), libbpp-seq-dev (>= 2.3.1)
Section: libdevel
Priority: optional
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Description: Bio++ Phylogenetic library development files
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
Bio++ is Object Oriented and is designed to be both easy to use and
computer efficient. Bio++ intends to help programmers to write computer
expensive programs, by providing them a set of re-usable tools.
.
This package contains the static library and the header files of the
Bio++ classes for phylogenetics.
drwxr-xr-x root/root 0 2017-08-23 21:32 ./
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/Phyl/
-rw-r--r-- root/root 3681 2017-06-07 16:41 ./usr/include/Bpp/Phyl/AncestralStateReconstruction.h
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/Phyl/App/
-rw-r--r-- root/root 30993 2017-06-07 16:41 ./usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
-rw-r--r-- root/root 8180 2017-06-07 16:41 ./usr/include/Bpp/Phyl/BipartitionList.h
-rw-r--r-- root/root 6542 2017-06-07 16:41 ./usr/include/Bpp/Phyl/BipartitionTools.h
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/Phyl/Distance/
-rw-r--r-- root/root 7655 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
-rw-r--r-- root/root 3916 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/BioNJ.h
-rw-r--r-- root/root 19600 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/DistanceEstimation.h
-rw-r--r-- root/root 3371 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/DistanceMethod.h
-rw-r--r-- root/root 4014 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h
-rw-r--r-- root/root 4217 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/NeighborJoining.h
-rw-r--r-- root/root 4114 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Distance/PGMA.h
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/Phyl/Graphics/
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-rw-r--r-- root/root 9618 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
-rw-r--r-- root/root 6287 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
-rw-r--r-- root/root 3483 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h
-rw-r--r-- root/root 3241 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h
-rw-r--r-- root/root 3792 2017-06-07 16:41 ./usr/include/Bpp/Phyl/PatternTools.h
-rw-r--r-- root/root 3691 2017-06-07 16:41 ./usr/include/Bpp/Phyl/PhyloStatistics.h
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/include/Bpp/Phyl/Simulation/
-rw-r--r-- root/root 8235 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
-rw-r--r-- root/root 2583 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
-rw-r--r-- root/root 12789 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/MutationProcess.h
-rw-r--r-- root/root 10895 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
-rw-r--r-- root/root 4213 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h
-rw-r--r-- root/root 2363 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h
-rw-r--r-- root/root 2515 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Simulation/SiteSimulator.h
-rw-r--r-- root/root 5513 2017-06-07 16:41 ./usr/include/Bpp/Phyl/SitePatterns.h
-rw-r--r-- root/root 4190 2017-06-07 16:41 ./usr/include/Bpp/Phyl/TopologySearch.h
-rw-r--r-- root/root 15366 2017-06-07 16:41 ./usr/include/Bpp/Phyl/Tree.h
-rw-r--r-- root/root 7695 2017-06-07 16:41 ./usr/include/Bpp/Phyl/TreeExceptions.h
-rw-r--r-- root/root 20203 2017-06-07 16:41 ./usr/include/Bpp/Phyl/TreeTemplate.h
-rw-r--r-- root/root 44287 2017-06-07 16:41 ./usr/include/Bpp/Phyl/TreeTemplateTools.h
-rw-r--r-- root/root 29830 2017-06-07 16:41 ./usr/include/Bpp/Phyl/TreeTools.h
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/
-rw-r--r-- root/root 1610 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-config-version.cmake
-rw-r--r-- root/root 2311 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-config.cmake
-rw-r--r-- root/root 1515 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets-none.cmake
-rw-r--r-- root/root 3939 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl/bpp-phyl-targets.cmake
-rw-r--r-- root/root 29649388 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/libbpp-phyl.a
lrwxrwxrwx root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/libbpp-phyl.so -> libbpp-phyl.so.11
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl-dev/
-rw-r--r-- root/root 1690 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl-dev/changelog.Debian.gz
-rw-r--r-- root/root 7452 2017-06-07 16:41 ./usr/share/doc/libbpp-phyl-dev/changelog.gz
-rw-r--r-- root/root 3116 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl-dev/copyright
libbpp-phyl11-dbgsym_2.3.1-10_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 29496384 bytes: control archive=476 bytes.
410 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libbpp-phyl11-dbgsym
Source: libbpp-phyl
Version: 2.3.1-10
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 29954
Depends: libbpp-phyl11 (= 2.3.1-10)
Section: debug
Priority: extra
Multi-Arch: same
Description: Debug symbols for libbpp-phyl11
Build-Ids: 56ec4f86033d86fa404d9cd706e745ab739af569
drwxr-xr-x root/root 0 2017-08-23 21:32 ./
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/debug/.build-id/56/
-rw-r--r-- root/root 30661808 2017-08-23 21:32 ./usr/lib/debug/.build-id/56/ec4f86033d86fa404d9cd706e745ab739af569.debug
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl11-dbgsym -> libbpp-phyl11
libbpp-phyl11_2.3.1-10_armhf.deb
--------------------------------
new debian package, version 2.0.
size 1230092 bytes: control archive=939 bytes.
846 bytes, 19 lines control
313 bytes, 4 lines md5sums
29 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libbpp-phyl11
Source: libbpp-phyl
Version: 2.3.1-10
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5839
Depends: libbpp-core3, libbpp-seq11, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Description: Bio++ Phylogenetic library
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
Bio++ is Object Oriented and is designed to be both easy to use and
computer efficient. Bio++ intends to help programmers to write computer
expensive programs, by providing them a set of re-usable tools.
.
This package contains the Bio++ classes for phylogenetics.
drwxr-xr-x root/root 0 2017-08-23 21:32 ./
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11 -> libbpp-phyl.so.11.0.0
-rw-r--r-- root/root 5952952 2017-08-23 21:32 ./usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.11.0.0
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl11/
-rw-r--r-- root/root 1690 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl11/changelog.Debian.gz
-rw-r--r-- root/root 7452 2017-06-07 16:41 ./usr/share/doc/libbpp-phyl11/changelog.gz
-rw-r--r-- root/root 3116 2017-08-23 21:32 ./usr/share/doc/libbpp-phyl11/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 864564
Build-Time: 6168
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 389
Job: libbpp-phyl_2.3.1-10
Machine Architecture: armhf
Package: libbpp-phyl
Package-Time: 6607
Source-Version: 2.3.1-10
Space: 864564
Status: successful
Version: 2.3.1-10
--------------------------------------------------------------------------------
Finished at 2017-08-31T16:44:56Z
Build needed 01:50:07, 864564k disc space